Nanochannel-based DNA Barcoding for Plasmid Characterisation

Plasmids are circular DNA molecules found in bacteria. These molecules often contain genes coding for resilience against harmful substances such as antibiotics, in its environment. To be able to classify plasmids fast, and with small samples would be of great gain for medical care, to improve the efficiency of treatments, and to reduce the spread of antibiotics resistance. Our experimental collaborators (Fredrik Westerlund group, Chalmers) stain DNA molecules in a predictable way with a fluorescent chemical, and by doing so they create patterns (barcodes) for plasmids, which are observed through microscopes. We use the transfer matrix method to compute predicted barcodes from genetic sequences. By comparing barcodes, both from theory and from experiments, we identify types of plasmids, and find manipulations to the plasmids, such as missing or added genes. By combining barcodes with more conventional sequencing, the barcodes are used as scaffolds for the shorter fragments.För bakterier kostar det energi och tid att ha oanvändbart genetiskt material, och det är dessutom i vägen i en redan trång cell. Därför bör man göra sig av med onödigt material. Men på samma sätt som man tror sig snart kunna komma att behöva de sakerna som så länge stått och ”samlat damm i garderoben”, så är akterier ovilliga att kasta bort fullt fungerande gener. Dessa gener samlar de i så kallade plasmider, som är ringformade DNA-molekyler med syftet att ta hand om oanvändbara gener. Men till skillnad från de torkade färgresterna i burkarna i garderoben, så visar det sig att det finns tillfällen där lasmidgenerna är nyttiga. Till exempel kan det finnas en gen som skapar pumpar i bakteriens cellvägg. Dessa pumpar kan pumpa ut farliga tungmetaller, som annars hade skadat cellen. Om bakteriekolonin av någon anledning får tungmetaller i sin omgivning, så kommer de celler som inte har tillgång till den vanligtvis onödiga genen för metallpumpen att dö, medan de andra lever vidare utan några större problem. Eftersom så många av bakterierna i kolonin har dött, så kommer de kvarvarande cellerna snarare ha det lättare eftersom det finns mindre konkurrens om utrymme och resurser. På så sätt kommer alla levande bakterier i området snart vara resistenta, plasmiderna kan nämligen skickas mellan individer. Dessa individer behöver inte ens vara av samma art. Ett relaterat och, för människor, växande problem är när bakterier blir resistenta mot läkemedel, så som mot antibiotika. Är man oförsiktig kan man öka nyttan med en gen som ger resistens mot en sorts antibiotika, som därmed kommer bli verkningslös. Vad man kan göra för att hindra det är att innan kuren undersöka plasmiderna, för att avgöra vilken genuppsättning de har. Utifrån vad man ser där kan man välja den lämpligaste kuren. För det traditionella sättet att undersöka plasmiderna på behöver man odla bakterierna under en tid, så att tillräckligt många plasmider finns i provet. Därefter klipper man sönder plasmiderna och undersöker vad man har i provet. Ett problem med detta är att plasmider ändrar sig snabbt, och påverkas av miljön i vilken bakterien lever. Om en patient har resistenta bakterier i sig, så kan problemet verka mindre allvarligt än vad det är, eftersom bakterieprovet odlas i en antibiotikafri miljö. I den miljön är det en nackdel att ha resistensen, eftersom den inte hjälper, och den kommer därför delvis att försvinna. På så sätt kommer provresultatet vara missvisande. Vad man vill kunna göra är att omedelbart plocka ut individuella plasmider, och läsa av vilka gener den innehåller. Något man kan göra för att uppnå detta är att göra plasmiden till en streckkod. Det finns olika tekniker för det, bland annat så kallad ”competitive binding”. Det går till på så vis att man placerar plasmiden i ett kemikaliebad. I detta bad finns bland annat en sorts kemikalie som fastnar på plasmiden, men bara på vissa specifika platser. Badet innehåller också ett självlysande ämne. Detta ämne kan också sätta sig på plasmiden, men är inte lika noggran med var den sitter. Därför kommer det självlysande ämnet att fylla upp resten av plasmiden. Om man sen tittar på plasmiden i mikroskop, så kan man inte bara se att den lyser, men också att olika delar lyser olika mycket. Med hjälp av en metod som kallas ”överföringsmatris-metoden” kan man beräkna ett förväntat utseende på en given DNA-sekvens. Genom att jämföra dessa teoretiska streckkoder med experiment kan man komma fram till plasmiders innehåll. Detta går att göra på mindre än en timme efter att provet togs, vilket är mycket snabbare än andra metoder. I denna uppsats vidareutvecklar vi tidigare studier genom att skapa en karta över likheten mellan alla drygt 2 000 kända plasmider. Vi utvecklar också en metod för att upptäcka om en plasmid har ändrats, till exempel genom att DNA har flyttat på sig eller vänt sig. Vi har även en metod för att använda streckkoderna som mallar, när man vill bygga ihop en plasmid från kortare DNA-bitar. Sådana bitar är resultatet av andra analysmetoder, och att kombinera metoder är en viktig teknik för att komma runt svagheter som de enskilda metoderna har

Using Linear Splines to Continuously Develop Understanding of Affordances

Understanding affordance is a bottom-up process that lets simple visual features be used as clues on how to use an object, so that reasonable interactions with objects can be achieved, without any semantic knowledge. Linear splines are proposed as a way for robots to fast and continuously learn how their actions affect their surroundings. The general conclusions that they can draw from only little experience, using this method, are seen as an example of understanding affordances, and the specific case investigated by the robot created as a part of this thesis, is how pushing actions affect small blocks. This information will be used by the robot to perform goal directed tasks, namely to push the block to specific predetermined positions. A way to make generalised predictions, so that actions on new shapes can be performed in a reasonable way without any previous interaction, is proposed. It becomes obvious that good inner representations of actions and reactions are necessary, as well as some management of learned relations

Genes with Relevance for Early to Late Progression of Colon Carcinoma Based on Combined Genomic and Transcriptomic Information from the Same Patients

Background: Genetic and epigenetic alterations in colorectal cancer are numerous. However, it is difficult to judge whether such changes are primary or secondary to the appearance and progression of tumors. Therefore, the aim of the present study was to identify altered DNA regions with significant covariation to transcription alterations along colon cancer progression. Methods: Tumor and normal colon tissue were obtained at primary operations from 24 patients selected by chance. DNA, RNA and microRNAs were extracted from the same biopsy material in all individuals and analyzed by oligo-nucleotide array-based comparative genomic hybridization (CGH), mRNA- and microRNA oligo-arrays. Statistical analyses were performed to assess statistical interactions (correlations, co-variations) between DNA copy number changes and significant alterations in gene and microRNA expression using appropriate parametric and non-parametric statistics. Results: Main DNA alterations were located on chromosome 7, 8, 13 and 20. Tumor DNA copy number gain increased with tumor progression, significantly related to increased gene expression. Copy number loss was not observed in Dukes A tumors. There was no significant relationship between expressed genes and tumor progression across Dukes A–D tumors; and no relationship between tumor stage and the number of microRNAs with significantly altered expression. Interaction analyses identified overall 41 genes, which discriminated early Dukes A plus B tumors from late Dukes C plus D tumor; 28 of these genes remained with correlations between genomic and transcriptomic alterations in Dukes C plus D tumors and 17 in Dukes D. One microRNA (microR-663) showed interactions with DNA alterations in all Dukes A-D tumors. Conclusions: Our modeling confirms that colon cancer progression is related to genomic instability and altered gene expression. How- ever, early invasive tumor growth seemed rather related to transcriptomic alterations, where changes in microRNA may be an early phenomenon, and less to DNA copy number changes

A 3D cellular context for the macromolecular world

We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community

Driver adherence to recommendations from support systems improves if the systems explain why they are given: a simulator study

This paper presents a large-scale simulator study on driver adherence to recommendations given by driver support systems, specifically eco-driving support and navigation support. 123 participants took part in this study, and drove a vehicle simulator through a pre-defined environment for a duration of approximately 10 min. Depending on the experimental condition, participants were either given no eco-driving recommendations, or a system whose provided support was either basic (recommendations were given in the form of an icon displayed in a manner that simulates a heads-up display) or informative (the system additionally displayed a line of text justifying its recommendations). A navigation system that likewise provided either basic or informative support, depending on the condition, was also provided. Effects are measured in terms of estimated simulated fuel savings as well as engine braking/coasting behaviour and gear change efficiency. Results indicate improvements in all variables. In particular, participants who had the support of an eco-driving system spent a significantly higher proportion of the time coasting. Participants also changed gears at lower engine RPM when using an eco-driving support system, and significantly more so when the system provided justifications. Overall, the results support the notion that providing reasons why a support system puts forward a certain recommendation improves adherence to it over mere presentation of the recommendation. Finally, results indicate that participants’ driving style was less eco-friendly if the navigation system provided justifications but the eco-system did not. This may be due to participants considering the two systems as one whole rather than separate entities with individual merits. This has implications for how to design and evaluate a given driver support system since its effectiveness may depend on the performance of other systems in the vehicle

Perceiving agents : Pluralism, interaction, and existence

Perception is a vast subject to study. One way to approach and study it might therefore be to break down the concept into smaller pieces. Specific modes of sensation, mechanisms, phenomena, or contexts might be selected as the proxy or starting point for addressing perception as a whole. Another approach would be to widen the concept, and attempt to study perception through the larger context of which it is a part. I have, in this thesis, attempted the latter strategy, by emphasising an existential perspective, and examine the role and nature of perception through that lens. The larger perspective of broadening the scope does not specifically allow for better answers, but rather different kinds of answers, providing complementary ways of exploring what it means to be an artificial or natural agent, and what consequences that can have for the access to, as well as representation, processing, and communication of information. A broader stance can also facilitate exploration of questions regarding larger perspectives, such as the relation between individual agents, as well as their place in larger structures such as societies and cyber-physical systems. In this thesis I use existential phenomenology to frame the concept of perception, while drawing from theories in biology and psychology. My work has a particular focus on human-robot interaction, a field of study at a fascinating intersection of humans designing, using, and communicating with something human-made, partially human-like, yet distinctly non-human. The work is also applied to some aspects of the traffic domain which, given the increasing interest in self-driving vehicles, is partially another instance of complex and naturalistic human-robot interaction. Ultimately, I argue for a pluralistic and pragmatic approach to the understanding of perception, and its related concepts. To understand a system of agents as they interact, it is not only necessary to acknowledge their respective circumstances, but take serious the idea that none of the agents’ constructed worlds are more or less real, they might only be more or less relevant in relation to specific contexts, perspectives, or needs. Such an approach is particularly relevant when addressing the complexities of the increasingly urgent sustainability challenges.Perception är ett enormt brett ämne att studera. Ett sätt att närma sig ämnet är därför att bryta ner konceptet i mindre delar. Specifika sinnen, mekanismer, fenomen eller sammanhang kan då väljas ut som representanter eller som startpunkter för att närma sig perception som helhet. Ett annat sätt är att istället bredda konceptet och försöka studera perception genom det större sammanhang som det är del av. Jag har i denna avhandling valt den senare strategin, genom att betona ett existentiellt perspektiv och undersöka perceptionens roll och natur genom den linsen. Att bredda perspektivet innebär inte specifikt bättre svar, utan snarare andra sorters svar. Detta bidrar i sin tur med kompletterande sätt att utforska vad det innebär att vara en artificiell eller naturlig agent, och vilka konsekvenser det kan ha i termer av tillgång till, såväl som representation, bearbetning och kommunikation av, information. Ett breddat synsätt kan dessutom underlätta utforskandet av frågor gällande större perspektiv såsom relationen mellan individuella agenter och deras plats i större strukturer såsom samhällen och cyberfysiska system. I denna avhandling använder jag den teoretiska utgångspunkten existentiell fenomenologi för att rama in konceptet perception, men jag förlitar mig också på teorier från biologi och psykologi. Mer praktiskt har jag tillämpat dessa teorier på människa-robotinteraktion, vilket är ett ämne som uppstår i mötet mellan människor som skapar, använder och kommunicerar med något som är tillverkat av människor, som delvis är människolikt men samtidigt är distinkt icke-mänskligt. Jag har också tillämpat teorierna på några aspekter av trafikdomänen vilket delvis, givet det ökande intresset för självkörande fordon, kan ses som en instans av komplex och naturalistisk människa-robotinteraktion. Slutligen argumenterar jag för ett pluralistiskt och pragmatiskt tillvägagångssätt för att förstå perception och dess relaterade koncept. I system av interagerande agenter är det inte bara nödvändigt att erkänna deras respektive förutsättningar. Det är också viktigt att på allvar ta idén om att ingen agents konstruerade värld är mer eller mindre verklig, de är bara mer eller mindre relevanta i relation till specifika sammanhang, perspektiv eller behov. Ett pluralistiskt och pragmatiskt tillvägagångssätt är än mer relevant för att bemöta de alltmer brådskande hållbarhetsutmaningarna

Global disease transmission - What if SARS would have been more lethal?

Global disease transmission is an important area, since knowledge of the time of the onset of an epidemic in a region might help authorities to save many lives. In this thesis I have used a deterministic model with eight parameters, of which two were time dependent, for spreading of the SARS disease. My model is an extension of a model by Colizza and co-workers, where I have added a Heaviside step function, that prevent latent people to interact if they are to few. I have also added a ”repulsion factor”, that reduces the traffic to an infected city. In my model I used data on how 3,147 of the airports of the world are connected. The strength of the connections were not given, so they were estimated, using the population sizes of the cities. The corresponding rate equations was solved by computer programs, written by me in Java, one of which displayed the result on a map. A major finding of this thesis is that vaccination can be used to prevent an epidemic from fully break out, and the doses are preferably concentrated to well connected regions, although the effect is not dramatical. This is demonstrated by comparing the effect of vaccinating London, with the effect of vaccinating Tianjin, and with the effect of vaccinating New York. I also demonstrate that the latency of a disease is an important factor for mortality of a disease

Speaking Properly with Robots

There is a risk of genuine but norm-breaking phenomena related to human-robot interaction remaining invisible, since their rarity make observed instances dismissed as anecdotes. In this extended abstract we present observations related to bias in who is understood in vocal interactions with robots. Noting the fundamentally political and intersectional nature of the problem, we call for a strategy for documenting such comparatively rare or messy events to break the invisibility and facilitate accumulation of evidence

Conceptual Tools for Exploring Perspectives of Different Kinds of Road-Users

The traffic domain is increasingly inhabited by vehicles with driving support systems and automation to the degree where the idea of fully autonomous vehicles is gaining popularity as a credible prediction about the near future. As more aspects of driving become automated, the role of the driver, and the way they perceive their vehicle, surroundings, and fellow road users, change. To address some of the emerging kinds of interaction between different agents in the traffic environment, it is important to take social phenomena and abilities into account, even to the extent of considering highly automated vehicles to be social agents in their own right. To benefit from that, it is important to frame the perception of the traffic environment, as well as the road users in it, in an appropriate theoretical context. We propose that there are helpful concepts related to functional and subjective perception, derived from gestalt psychology and Umweltlehre, that can fill this theoretical need, and support better understanding of vehicles of various degrees of automation

Do Tourists Dream of Electric Bikes? : Electric Bikes as a Mean to Improve Sustainability of Tourism in Rural Sweden

The paper investigates the potential of electric bikes as a sustainable alternative for local transportation during vacations in rural areas, replacing mainly transportation by car. Our starting point is that a key to behaviour change in the context of tourism and leisure travels is to make the sustainable travel option the most desirable option for the traveller. We study this by exploring three different electric bike offers in the area of Skaraborg, Sweden, and analysing the experience of the cyclists. 15 participants were invited to rent electric bicycles as mode of transportation for tourism in and around the small towns Lidköping and Skara for one day. Individual semi structured interviews were performed with the participants. Our main result is that there are aspects of electric bikes that make them particularly appropriate as a sustainable mode of transportation for local tourist destinations, and could also lower the threshold for more sustainable behaviours. Travelling by electric bike was experienced as beneficial in several ways; it automatically and effortlessly gives the cyclist access to nature, it constitutes a plausible option for more sustainable transportation at medium distances, and it allows the entire group of travellers, such as a families, to feel as being part of shaping the journey which contributes to engagement and motivation. Although intended for tourists, it also facilitate local people to access and reflect on their local flora and fauna. We also found that digital tools such as maps, information sources, and booking systems have a key part in the deployment when appropriately integrated. In addition, we found that it was important to lower the threshold of trying electric bikes, and an important key for this was personal service from proficient people who could provide a sense of security by giving instructions, answering questions, and support in adjusting the equipment.CC BY 4.0This work is done within the Interreg funded project SMaRT —Sustainable Mobility Rural and Urban Transport, NYPS 20203416. The authors would also like to thank Kajsa Nalin who assisted in taking the teaser image.SMaRT — Sustainable Mobility Rural and Urban Transpor